Mon Oct 10 19:41:25 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 19:41:25 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2736 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6421820 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 13.65100 62.65700 ymin,ymax (A): -18.26400 37.17200 zmin,zma (A): 31.22700 84.59900 x,y,z range (A): 49.00600 55.43600 53.37200 scale (grids/A): 0.6421820 object centre (A): 38.15400 9.454000 57.91300 number of atom coordinates read : 2736 total number of charged atoms : 2597 net assigned charge : 6.500029 assigned positive charge : 409.9234 centred at (gu) : 91.59841 92.97061 89.64326 assigned negative charge : -403.4245 centred at (gu) : 91.57695 93.06423 89.57226 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7525 nv = 96 ne = 84 npr = 55928 no. pairs analyzed = 55928 no. exposed pairs = 3447 no. arc points = 24675 no. surface atoms = 1156 nbur = 1580 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 434 mr = 4028 m= 4 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3873 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2454 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 9089 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3146952E-09 1.7879161E-08 midg,1,midg; midg,igrid,midg 1.1897686E-08 -3.9067727E-09 1,midg,midg; igrid,midg,midg 5.5238965E-09 1.8276173E-08 gauss-seidel spectral radius is 0.9874516 estimated iterations to convergence 73 setup time was (sec) 0.3900000 now iterating at: 19:41:26 rms-change max change #iterations 0.1494394 22.85494 at 10iterations 1.4760942E-02 2.104776 at 20iterations 1.4539071E-03 0.2016621 at 30iterations 1.4674610E-04 1.9325256E-02 at 40iterations 1.5185486E-05 2.0275116E-03 at 50iterations finished qdiffx linear iterations at : 19:41:29 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.5185486E-05 2.0275116E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 19:41:29 3.390u 0.185s 0:03.87 92.2% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 19:41:29 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2736 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.926546 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 13.65100 62.65700 ymin,ymax (A): -18.26400 37.17200 zmin,zma (A): 31.22700 84.59900 x,y,z range (A): 49.00600 55.43600 53.37200 scale (grids/A): 1.926546 object centre (A): 38.15400 9.454000 57.91300 number of atom coordinates read : 2736 total number of charged atoms : 2597 net assigned charge : 6.500029 assigned positive charge : 409.9234 centred at (gu) : 94.79462 98.91113 88.92892 assigned negative charge : -403.4245 centred at (gu) : 94.73086 99.19244 88.71653 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80678 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24675 grid for indexing accessible points = 1.400000 m= 28828 mr = 55059 m= 5121 mr = 20770 m= 354 mr = 3179 m= 6 mr = 149 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 349 time to turn everything in is 0.4000000 number of dielectric boundary points 35830 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 149 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 20426 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6421820 object centre at (A) : 38.15400 9.454000 57.91300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0541839E-02 3.5655107E-02 midg,1,midg; midg,igrid,midg 5.1574935E-03 2.7985157E-02 1,midg,midg; igrid,midg,midg 1.2439566E-02 1.9590165E-02 gauss-seidel spectral radius is 0.9986797 estimated iterations to convergence 218 setup time was (sec) 0.6100000 now iterating at: 19:41:30 rms-change max change #iterations 4.448349 192.3915 at 10iterations 2.105192 82.21487 at 20iterations 0.9916568 28.81020 at 30iterations 0.4702677 14.68181 at 40iterations 0.2231088 8.318810 at 50iterations 0.1057161 3.269271 at 60iterations 4.9922515E-02 1.620318 at 70iterations 2.3720659E-02 0.7118607 at 80iterations 1.1256854E-02 0.3468323 at 90iterations 5.3247414E-03 0.1670332 at 100iterations 2.5301301E-03 7.7722549E-02 at 110iterations 1.2011890E-03 3.5470486E-02 at 120iterations finished qdiffx linear iterations at : 19:41:37 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 1.2011890E-03 3.5470486E-02 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 19:41:38 7.831u 0.215s 0:08.36 96.1% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 19:41:38 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2736 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.889819 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 13.65100 62.65700 ymin,ymax (A): -18.26400 37.17200 zmin,zma (A): 31.22700 84.59900 x,y,z range (A): 49.00600 55.43600 53.37200 scale (grids/A): 2.889819 object centre (A): 38.15400 9.454000 57.91300 number of atom coordinates read : 2736 total number of charged atoms : 2597 net assigned charge : 6.500029 assigned positive charge : 409.9234 centred at (gu) : 97.19164 103.3663 88.39320 assigned negative charge : -403.4245 centred at (gu) : 97.09620 103.7885 88.07477 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 186916 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24675 grid for indexing accessible points = 1.400000 m= 92251 mr = 133844 m= 34452 mr = 74448 m= 9195 mr = 27261 m= 1544 mr = 6898 m= 113 mr = 1107 m= 4 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 1255 time to turn everything in is 1.040000 number of dielectric boundary points 80862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 20775 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.926546 object centre at (A) : 38.15400 9.454000 57.91300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4591356E-02 0.2762607 midg,1,midg; midg,igrid,midg 9.6313216E-02 0.3463611 1,midg,midg; igrid,midg,midg 0.2205049 0.2141535 gauss-seidel spectral radius is 0.9992736 estimated iterations to convergence 293 setup time was (sec) 1.320000 now iterating at: 19:41:39 rms-change max change #iterations 10.33215 387.2454 at 10iterations 6.056666 133.4405 at 20iterations 3.523932 67.01593 at 30iterations 2.047477 35.65302 at 40iterations 1.191406 19.75901 at 50iterations 0.6892970 13.18865 at 60iterations 0.4003024 7.629271 at 70iterations 0.2313662 4.228256 at 80iterations 0.1338091 2.410816 at 90iterations 7.7533379E-02 1.336342 at 100iterations 4.4849891E-02 0.7992210 at 110iterations 2.5901891E-02 0.4546095 at 120iterations 1.4956668E-02 0.2639399 at 130iterations 8.6397026E-03 0.1457844 at 140iterations 4.9938862E-03 8.7936401E-02 at 150iterations 2.8923713E-03 4.9034119E-02 at 160iterations 1.6724345E-03 2.9693604E-02 at 170iterations 9.7102317E-04 1.7543793E-02 at 180iterations finished qdiffx linear iterations at : 19:41:52 total time elapsed so far: 14.58000 # loops : 180 mean,max change (kT/e) : 9.7102317E-04 1.7543793E-02 energy calculations done at 14.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.70000 DelPhi exited at 19:41:53 14.706u 0.260s 0:15.25 98.0% 0+0k 0+0io 0pf+0w